parse_batches: Read and parse doc of PubMed records and extract specified...
In maia-sh/pubmedparser: Fetch and Parse PubMed Records

Read and parse doc of PubMed records and extract specified datatypes as csv's

parse_batches(
  input_dir,
  pmids = NULL,
  datatypes = c("table", "abstract", "databanks", "authors", "mesh", "keywords",
    "pubtypes"),
  file_name = "pubmed",
  suffix = NULL,
  dir = here::here(),
  subdir = dir,
  quiet = FALSE,
  return = FALSE
)

`input_dir`	Filepath of doc of batch of unparsed PubMed records, such as the output of `fetch_batch`.
`pmids`	Vector of pmids. If pmids not user-provided, pmids will be saved as .rds.
`datatypes`	Types of data to extract from xml for which there is a corresponding "pubmed_" function ("table", "abstract", "databanks", "authors", "mesh", "keywords", "pubtypes")
`file_name`	and @param suffix If both are equal to default, `doc` is checked against filename patterns of files generated by `fetch_batch` (either "YYYY-MM-DD_FILENAME_SUFFIX.txt" or "YYYY-MM-DD_FILENAME.txt"). Available values are extracted.
`suffix`	Suffix for file names. For example, record numbers. Defaults to NULL.
`dir`	Directory for saving files (log file and pmids.rds, and extracted csv's, depending on `subdir`). Defaults to project root (`here::here()`)
`subdir`	Directory for saving extracted csv's. Defaults to `dir`.
`quiet`	Whether to silence messages in console. Defaults to FALSE.
`return`	Whether to return parsed xml. Defaults to FALSE since complete batches may be too large to hold in memory and interested in only side-effect csv's. If TRUE, returns list of length number of files in `input_dir` with each element containing a parsed xml.